PGS Publication: PGP000168

Publication Information (EuropePMC)
Title Evaluation of a Multiethnic Polygenic Risk Score Model for Prostate Cancer.
PubMed ID 33792693(Europe PMC)
doi 10.1093/jnci/djab058
Publication Date April 1, 2021
Journal J Natl Cancer Inst
Author(s) Plym A, Penney KL, Kalia S, Kraft P, Conti DV, Haiman C, Mucci LA, Kibel AS.
Released in PGS Catalog: April 28, 2021

Associated Polygenic Score(s)

Filter PGS by Participant Ancestry
Individuals included in:
G - Source of Variant Associations (GWAS)
D - Score Development/Training
E - PGS Evaluation
List of ancestries includes:
Display options:
Ancestry legend
Multi-ancestry (including European)
Multi-ancestry (excluding European)
African
East Asian
South Asian
Additional Asian Ancestries
European
Greater Middle Eastern
Hispanic or Latin American
Additional Diverse Ancestries
Not Reported

External PGS Evaluated By This Publication

Polygenic Score ID & Name PGS Publication ID (PGP) Reported Trait Mapped Trait(s) (Ontology) Number of Variants Ancestry distribution
GWAS
Dev
Eval
 Scoring File (FTP Link)
PGS000662
(GRS.PCa.269)
 PGP000122 |
Conti DV et al. Nat Genet (2021)
 Prostate cancer prostate carcinoma 269
-
 https://ftp.ebi.ac.uk/pub/databases/spot/pgs/scores/PGS000662/ScoringFiles/PGS000662.txt.gz

Performance Metrics

Disclaimer: The performance metrics are displayed as reported by the source studies. It is important to note that metrics are not necessarily comparable with each other. For example, metrics depend on the sample characteristics (described by the PGS Catalog Sample Set [PSS] ID), phenotyping, and statistical modelling. Please refer to the source publication for additional guidance on performance.

PGS Performance
Metric ID (PPM) 		Evaluated Score PGS Sample Set ID
(PSS) 		Performance Source Trait PGS Effect Sizes
(per SD change) 		Classification Metrics Other Metrics Covariates Included in the Model PGS Performance:
Other Relevant Information
PPM001951 PGS000662
(GRS.PCa.269)
 PSS000976|
European Ancestry|
12,472 individuals
 PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Prevalent prostate cancer OR: 2.04 — Odds ratio (OR, top 10% vs. middle 20%): 3.89 [3.24, 4.68] Age at blood collection, genotyping platform, PCs(1-10) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001952 PGS000662
(GRS.PCa.269)
 PSS000976|
European Ancestry|
12,472 individuals
 PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Prevalent prostate cancer — — Odds ratio (OR, bottom 10% vs. middle 20%): 0.34 [0.25, 0.46] Age at blood collection, genotyping platform, PCs(1-10) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001953 PGS000662
(GRS.PCa.269)
 PSS000976|
European Ancestry|
12,472 individuals
 PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Elevated prostate specific antigen OR: 1.54 — — Age at blood collection, genotyping platform, PCs(1-10) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001954 PGS000662
(GRS.PCa.269)
 PSS000975|
African Ancestry|
524 individuals
 PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Prevalent prostate cancer — — Odds ratio (OR, top 10% vs. middle 20%): 3.81 [1.48, 10.19] Age at blood collection, genotyping platform, PCs(1-2) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.
PPM001955 PGS000662
(GRS.PCa.269)
 PSS000975|
African Ancestry|
524 individuals
 PGP000168 |
Plym A et al. J Natl Cancer Inst (2021)
|Ext.		 Reported Trait: Prevalent prostate cancer — — Odds ratio (OR, bottom 10% vs. middle 20%): 0.15 [0.01, 0.92] Age at blood collection, genotyping platform, PCs(1-2) Only 261 of the original 269 SNPs were available for analysis due to no imputation of the X chromosome.

Evaluated Samples

PGS Sample Set ID
(PSS) 		Phenotype Definitions and Methods Participant Follow-up Time Sample Numbers Age of Study Participants Sample Ancestry Additional Ancestry Description Cohort(s) Additional Sample/Cohort Information
PSS000975 Cases were defined as having a biopsy-confirmed prostate cancer documented by a pathology report or at least two prostate cancer-related billing codes any time before or within 6 months of the date of blood collection. —
[
  • 67 cases
  • , 457 controls
]
,
100.0 % Male samples
 — African unspecified — MGBB Formerly known as Partners healthcare Biobank (PHB)
PSS000976 Cases were defined as having a biopsy-confirmed prostate cancer documented by a pathology report or at least two prostate cancer-related billing codes any time before or within 6 months of the date of blood collection. —
[
  • 1,554 cases
  • , 10,918 controls
]
,
100.0 % Male samples
 — European — MGBB Formerly known as Partners healthcare Biobank (PHB)